GapMind for catabolism of small carbon sources

 

Alignments for a candidate for frcA in Burkholderia phytofirmans PsJN

Align Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized)
to candidate BPHYT_RS30865 BPHYT_RS30865 sugar ABC transporter ATP-binding protein

Query= SwissProt::Q9F9B0
         (260 letters)



>FitnessBrowser__BFirm:BPHYT_RS30865
          Length = 256

 Score =  176 bits (445), Expect = 6e-49
 Identities = 100/223 (44%), Positives = 144/223 (64%), Gaps = 6/223 (2%)

Query: 7   LTARGLVKRYGRVTALDRADFDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDEGEIRLE 66
           L    +VKR+G VTALD     L  GEIL V+GDNGAGKS++IK ++G      G++ + 
Sbjct: 8   LRGEDIVKRFGAVTALDGVSLTLKQGEILGVLGDNGAGKSTLIKILTGFHQQTSGKLFVG 67

Query: 67  GKPIQFRSPMEARQAGIETVYQNLALSPALSIADNMFLGREIRKPGIMGKWFRSLDRAAM 126
           G+    RS   AR  GIE VYQ+LAL+ +LSI  NMFL REI + G     FR LD  AM
Sbjct: 68  GEETMLRSVDHARSLGIECVYQDLALANSLSIYHNMFLNREIIRRGP----FRLLDNRAM 123

Query: 127 EKQARAKLSELGLMTIQNINQAVETLSGGQRQGVAVARAAAFGSKVVIMDEPTAALGVKE 186
            ++A   L E+G + + +++  VE LSGGQRQ +AVARA    +K++++DEP AA+G +E
Sbjct: 124 RERAAECLEEIG-VHVPSVDLPVEQLSGGQRQAIAVARAVNSNAKILLLDEPLAAMGARE 182

Query: 187 SRRVLELILDVRRR-GLPIVLISHNMPHVFEVADRIHIHRLGR 228
           +  +++LIL ++ + GL IV+I HN     ++ADR+ + + GR
Sbjct: 183 AGLIIDLILRLKAKGGLSIVMIMHNYAQTLDIADRVMLMQRGR 225


Lambda     K      H
   0.321    0.136    0.383 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 153
Number of extensions: 6
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 260
Length of database: 256
Length adjustment: 24
Effective length of query: 236
Effective length of database: 232
Effective search space:    54752
Effective search space used:    54752
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 47 (22.7 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory